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- PDB-2oq0: Crystal Structure of the First HIN-200 Domain of Interferon-Induc... -

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Basic information

Entry
Database: PDB / ID: 2oq0
TitleCrystal Structure of the First HIN-200 Domain of Interferon-Inducible Protein 16
ComponentsGamma-interferon-inducible protein Ifi-16
KeywordsPROTEIN BINDING / OB folds / beta-barrels / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


negative regulation of AIM2 inflammasome complex assembly / negative regulation of cysteine-type endopeptidase activity / STING mediated induction of host immune responses / myeloid cell differentiation / activation of cysteine-type endopeptidase activity / IRF3-mediated induction of type I IFN / negative regulation of gene expression, epigenetic / negative regulation of viral genome replication / negative regulation of DNA binding / monocyte differentiation ...negative regulation of AIM2 inflammasome complex assembly / negative regulation of cysteine-type endopeptidase activity / STING mediated induction of host immune responses / myeloid cell differentiation / activation of cysteine-type endopeptidase activity / IRF3-mediated induction of type I IFN / negative regulation of gene expression, epigenetic / negative regulation of viral genome replication / negative regulation of DNA binding / monocyte differentiation / transcription factor binding / intrinsic apoptotic signaling pathway by p53 class mediator / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / cellular response to interferon-beta / cellular response to glucose starvation / activation of innate immune response / negative regulation of innate immune response / positive regulation of interleukin-1 beta production / regulation of autophagy / cellular response to ionizing radiation / positive regulation of cytokine production / autophagy / double-stranded DNA binding / defense response to virus / nuclear speck / inflammatory response / innate immune response / negative regulation of DNA-templated transcription / nucleolus / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
HIN-200/IF120x / HIN-200 family / HIN-200/IF120x domain / HIN-200 A and B domains profile. / DAPIN domain / DAPIN domain profile. / PAAD/DAPIN/Pyrin domain / PAAD/DAPIN/Pyrin domain / Death-like domain superfamily / Nucleic acid-binding proteins ...HIN-200/IF120x / HIN-200 family / HIN-200/IF120x domain / HIN-200 A and B domains profile. / DAPIN domain / DAPIN domain profile. / PAAD/DAPIN/Pyrin domain / PAAD/DAPIN/Pyrin domain / Death-like domain superfamily / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Gamma-interferon-inducible protein 16
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsLam, R. / Liao, J.C.C. / Ravichandran, M. / Ma, J. / Tempel, W. / Chirgadze, N.Y. / Arrowsmith, C.H. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of the First HIN-200 Domain of Interferon-Inducible Protein 16
Authors: Liao, J.C.C. / Lam, R. / Ravichandran, M. / Ma, J. / Tempel, W. / Chirgadze, N.Y. / Arrowsmith, C.H.
History
DepositionJan 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gamma-interferon-inducible protein Ifi-16
B: Gamma-interferon-inducible protein Ifi-16
C: Gamma-interferon-inducible protein Ifi-16
D: Gamma-interferon-inducible protein Ifi-16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,6555
Polymers96,6204
Non-polymers351
Water2,864159
1
A: Gamma-interferon-inducible protein Ifi-16


Theoretical massNumber of molelcules
Total (without water)24,1551
Polymers24,1551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Gamma-interferon-inducible protein Ifi-16


Theoretical massNumber of molelcules
Total (without water)24,1551
Polymers24,1551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Gamma-interferon-inducible protein Ifi-16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1902
Polymers24,1551
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Gamma-interferon-inducible protein Ifi-16


Theoretical massNumber of molelcules
Total (without water)24,1551
Polymers24,1551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.335, 88.959, 112.831
Angle α, β, γ (deg.)90.000, 99.370, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Gamma-interferon-inducible protein Ifi-16 / Interferon-inducible myeloid differentiation transcriptional activator / IFI 16


Mass: 24154.961 Da / Num. of mol.: 4 / Fragment: First HIN200 Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IFI16, IFNGIP1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Condon-Plus / References: UniProt: Q16666
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 26% PEG 6000, 0.1M TRIS-HCl pH 8.5, 0.2M MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 9, 2006
RadiationMonochromator: Cryogenically-cooled Si(111) double-crystal system
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 57163 / Num. obs: 55105 / % possible obs: 96.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.1 % / Biso Wilson estimate: 32.1 Å2 / Rmerge(I) obs: 0.072 / Χ2: 2.671 / Net I/σ(I): 14.3
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 2.7 / Num. unique all: 4915 / Rsym value: 0.389 / Χ2: 0.764 / % possible all: 85.7

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Phasing

PhasingMethod: SAD
Phasing MAD set
IDR cullis acentricR cullis centricHighest resolution (Å)Lowest resolution (Å)Reflection acentricReflection centric
ISO_100247.19534321631
ANO_10.6850247.19515940
Phasing MAD set shell
IDResolution (Å)R cullis acentricR cullis centricReflection acentricReflection centric
ISO_18.8-47.190056172
ISO_16.27-8.800110190
ISO_15.14-6.2700145090
ISO_14.46-5.1400171089
ISO_13.99-4.4600194184
ISO_13.64-3.9900214284
ISO_13.38-3.6400234485
ISO_13.16-3.3800250688
ISO_12.98-3.1600265783
ISO_12.83-2.9800280386
ISO_12.69-2.8300298581
ISO_12.58-2.6900310483
ISO_12.48-2.5800321084
ISO_12.39-2.4800334281
ISO_12.31-2.3900349385
ISO_12.24-2.3100357478
ISO_12.17-2.2400367880
ISO_12.11-2.1700365276
ISO_12.05-2.1100367766
ISO_12-2.0500350266
ANO_18.8-47.190.32505090
ANO_16.27-8.80.299010680
ANO_15.14-6.270.355014090
ANO_14.46-5.140.444016630
ANO_13.99-4.460.488018800
ANO_13.64-3.990.494020840
ANO_13.38-3.640.523022710
ANO_13.16-3.380.587024700
ANO_12.98-3.160.645026270
ANO_12.83-2.980.698027780
ANO_12.69-2.830.762029690
ANO_12.58-2.690.833030770
ANO_12.48-2.580.883031930
ANO_12.39-2.480.933033180
ANO_12.31-2.390.951034580
ANO_12.24-2.310.973034940
ANO_12.17-2.240.985035640
ANO_12.11-2.170.991034090
ANO_12.05-2.110.996033090
ANO_12-2.051.002030440
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
1-15.06-17.881-54.319SE37.762.6
20.976-15.442-65.257SE39.952.47
36.3687.193-100.599SE40.862.13
412.217-31.13-74.277SE45.021.71
53.65315.205-122.243SE63.222.31
6-17.606-33.838-40.315SE45.651.78
713.454-21.995-94.2SE45.361.4
8-22.124-19.565-57.078SE50.881.72
98.7979.636-120.086SE40.911.2
1013.2127.704-97.025SE70.561.72
117.766-12.252-63.067SE58.821.26
12-3.82-38.156-40.527SE75.731.68
13-25.291-21.778-23.864SE69.031.48
14-23.801-24.216-65.563SE56.11
153.285-41.575-70.91SE84.441.73
16-22.708-41.592-39.035SE75.741.28
17-15.995-15.464-14.49SE107.211.63
1812.795-14.509-92.54SE60.480.86
192.93-26.063-104.353SE100.71.69
20-30.17-16.164-27.875SE87.051.01
21-22.729-34.244-76.843SE92.060.94
22-22.251-34.362-73.003SE87.110.93
23-9.161-22.183-107.717SE68.960.62
24-32.514-13.548-54.216SE64.010.58
25-0.923-29.864-10.376SE64.90.56
26-6.22-22.951-107.452SE64.90.53
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 55063
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
9.42-10065.10.693521
7.11-9.42630.854717
5.95-7.1160.80.859925
5.21-5.9559.10.891048
4.7-5.2157.60.9261183
4.31-4.755.20.9291289
4.01-4.3159.50.9211413
3.76-4.0158.40.9151505
3.55-3.7660.60.911557
3.37-3.55610.9061692
3.22-3.3760.50.8921750
3.09-3.2262.60.8861801
2.97-3.0961.60.881933
2.86-2.9766.60.8741945
2.77-2.8665.50.872044
2.68-2.7768.60.8662105
2.6-2.6869.20.8672168
2.53-2.669.80.8562228
2.47-2.5370.60.8622286
2.4-2.4774.40.8762332
2.35-2.473.90.8692384
2.29-2.3574.80.8742447
2.24-2.2976.60.882490
2.2-2.2479.80.882568
2.15-2.281.50.8942527
2.11-2.15820.8812599
2.07-2.1183.40.8762553
2.04-2.0784.70.7762504
2-2.0484.20.8132549

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
DM5phasing
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT2data extraction
JDirectordata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2→41.31 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.928 / SU B: 10.431 / SU ML: 0.142 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.208 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26 2783 5.1 %RANDOM
Rwork0.208 ---
all0.211 55055 --
obs0.211 55055 96.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 47.771 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å20.11 Å2
2---0.09 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 2→41.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6141 0 1 159 6301
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226264
X-RAY DIFFRACTIONr_angle_refined_deg1.3321.9648412
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3335757
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.06325.484279
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.583151288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7541521
X-RAY DIFFRACTIONr_chiral_restr0.0910.2968
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024493
X-RAY DIFFRACTIONr_nbd_refined0.2040.22457
X-RAY DIFFRACTIONr_nbtor_refined0.3060.24272
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2262
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1520.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.29
X-RAY DIFFRACTIONr_mcbond_it0.8231.53910
X-RAY DIFFRACTIONr_mcangle_it1.28726196
X-RAY DIFFRACTIONr_scbond_it1.85232599
X-RAY DIFFRACTIONr_scangle_it2.8594.52213
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 196 -
Rwork0.255 3378 -
obs-3574 84.49 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5635-0.5219-0.86792.8911-0.37744.75950.0978-0.0556-0.0639-0.0826-0.0153-0.0161-0.54110.0979-0.0826-0.01410.01410.0254-0.1309-0.0232-0.12020.40854.69695.67
22.45490.71790.23491.8662-0.04211.9638-0.13160.2451-0.09670.04270.0786-0.0424-0.04270.03610.053-0.226-0.0058-0.04710.0262-0.0212-0.0471-1.28723.32572.104
30.8623-0.7533-0.06653.62190.50371.21340.0960.02690.0031-0.4962-0.0709-0.0128-0.0705-0.0965-0.0251-0.0594-0.0021-0.0408-0.05380.0007-0.044113.39623.99246.028
41.87650.6978-1.8962.8422-1.03916.3765-0.19550.007-0.13320.0754-0.16720.0150.54980.25670.3627-0.17510.0216-0.0055-0.04290.0009-0.056123.12710.72198.425
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA12 - 20212 - 202
22BB12 - 20312 - 203
33CC11 - 20211 - 202
44DD13 - 20313 - 203

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